:Phenotypes in OWL

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This page is intended for people making use of the PATO Phenotypic Quality ontology or the PATO EQ formalism using the OWL ontology language.

This page is also supplemental material for the paper

Chris Mungall et al Representing Phenotypes in OWL Proceedings of the OWLED 2007 Workshop on OWL: Experience and Direction

See: [1]

Contents

PATO in OWL

The latest version of the ontology is available in OWL from this URL:

URIs are of the form http://purl.org/obo/owl/PATO#PATO_0000001, in accord with the OboInOwl recommendations

Currently PATO is a subclass hierarchy

PATO UO Constraints

The unit ontology is available in OWL here:

TODO: PATO-UO constraints (eg metre is a unit of length)

PATO BFO Constraints

An experimental bridging ontology containing additional OWL axioms constraing PATO qualities via BFO is available here:

Currently these are very minimal, and they are summarised in OWL abstract syntax, below:

Every PATO quality is a BFO quality:

Class(PATO_0000001 partial bfo:Quality)

All PATO "qualities of a continuant" inhere in a continuant:

Class(PATO_0001241 partial restriction(inheres_in someValuesFrom(snap:Continuant)))

(note: the status of quality of an occurrent w.r.t BFO still has to be resolved. See PATO:Qualities_of_an_occurrent)

Relational qualities are directed towards (depend on) some additional entity:

Class(PATO_0001238 partial restriction(towards someValuesFrom(bfo:Entity)))
Class(PATO_0001240 partial restriction(towards someValuesFrom(bfo:Entity)))

EQ formalism in OWL

The PATO EQ Formalism can be viewed as shorthand for writing OWL class expressions, with certain caveats. The translation from pheno-syntax to OWL is shown below (we use OWL Manchester Syntax)

Simple EQ case

 E= ?e Q= ?q

=>

 ?q THAT inheres_in SOME ?e

which has the equivalent in obo-format:

 intersection_of: ?q
 intersection_of: inheres_in ?e

Relational Qualities

 Q= ?q E2= ?e2

=>

 ?q THAT towards SOME ?e2

which has obo-format equivalent

 intersection_of: ?q
 intersection_of: towards ?e2

Caveat: the instance-level towards relation should be between an instance and a universal. For example, sensitivity towards chlorine should be read as sensitivity to all instances of the universal chlorine. Translating instance-universal relations as DL existentials is therefore incorrect, but is the best solution that avoids OWL Full

TODO

Units

Measurements

Comparative phenotypes

Durations and time

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